Training - H3ABioNet - Pan African Bioinformatics Network

H3ABioNet NABDA Node Training Course on Visual Analytics of Human Genome Variation Datasets

: Training; 08 December 2013; Hits: 9189

Course Overview: The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent.

Catalogues on human genome variants produced by large-scale human genome variation projects provide a wealth of genome variation datasets to conduct research on the genomics and environmental determinants of common diseases with the goal of improving the health of African populations. A recognized need is to promote computational skills among African researchers to facilitate genomics-based research on human disease and health across the continent. Visual analytics, the science of analytical reasoning supported by interactive visual interfaces, provides computational tools and techniques to foster collaboration in making sense of data of any size. Participants will be introduced to the focus areas of visual analytics and learn visual analytics skills by working with datasets from catalogues on human genome variation such as 1000 genomes, National Human Genome Research Institute (NHGRI) GWAS Catalog and the Database of Genomic Variations. The expectation is that participants will initiate collaboration among the H3Africa consortium projects. The course is open to staff and students in the H3Africa Consortium projects.

The successful applicant’s home institution/project shall be responsible for transportation (to and from Abuja), and accommodation (Bed and Breakfast) at Abuja, and dinners during their stay. The host institution (NABDA/FMST) shall provide, in addition to free tuition, Tea Breaks and lunches during the course.

Course Trainers
Dr. Raphael Isokpehi, Visual Analytics in Biology Curriculum Network, USA
Dr. Oyekanmi Nash, NABDA, Nigeria
Dr. Segun Fatumo, NABDA/SANGER
Atinuke Hassan, NABDA, Nigeria

Course Programme
Day 1: Monday, 29 July, 2013
Bioinformatics Research Categories
Definition, Focus Areas, Scope and Process of Visual Analytics
Hardware and Software for Visual Analytics
Hands-on Exercises

Day 2: Tuesday, 30 July, 2013
Introduction to Datasets of Catalogues on Human Gene Names
Hands-on Exercises

Day 3: Wednesday, 31 July, 2013
Introduction to Datasets of Catalogues on Human Genome Variation
Hands-on Exercises

Day 4: Thursday, 1 August, 2013
Collaborative Visual Analytics
Day 5: Friday, 2 August, 2013
Collaborative Visual Analytics
Course Evaluation

How to apply

To apply to attend the course please complete the application form found here:
http://surveys.h3abionet.org/visualanalytics
The application form will open on the 25th June and the deadline for applications is the 15th July 2013.
Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached

Training Materials Availability:

Training materials for this course are not currently available.

past , education

H3ABioNet Introduction to Bioinformatics using the eBioKit platform 29th of July to 2nd of August 2013 International Center for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya

: Training; 08 December 2013; Hits: 8695

eBioKit is a system for teaching bioinformatics, which is running multiple open source web services on an Apple Mac-mini where all databases are stored locally. This reduces the need for a fast internet connection while giving the users an opportunity to incorporate their data sets in widely used web services.
This course is aimed at familiarizing trainees with the multiple uses of ebiokit. The course will train members who are required to perform bioinformatics analysis of genetic and genomic data generated in the various H3Africa projects but most likely also in other projects in there respective institutions.
The course will be 5 days long and will cover both theoretical and practical aspects of a range of topics centered on the analysis of genetic and genomic data. An emphasis will be placed on allowing participants to develop hands-on experience with analyzing real data using ebiokit.
The course is open to all members of the H3A Bioinformatics Network as well as H3A Researchers who are seeking advanced bioinformatics training.

Course objectives

The course is composed of a range of topics aimed at providing participants with the necessary hands-on practical skills to be able to analyze genetic, genomic and metagenomic data. The course will include some basic linux programming and then offer a comprehensive overview of commonly used bioinformatics tools and databases available on the eBiokit system, such as for example Ensembl and Galaxy, a Web-based platform for data-intensive biomedical research.

Trainers

Prof. Erik Bongcam-Rudloff, SLU-Global Bioinformatics Centre, Sweden
Dr. Andreas Gisel, Institute for Biomedical Technologies, Italy
Dr. Anne Fischer, ICIPE, Kenya
Dr. Etienne de Villiers, KWTRP, Kenya
Rafael Hernández, Centro de Investigaciones Príncipe Felipe

Course programme

Monday

Introduction to Bioinformatics
How to use the eBioKit
UNIX command line

Tuesday

Introduction to Biological Databases
Basics of Blast search
Constructing your own searchable blast database
MRS: searching with names and keywords
Introduction to Genome Browsers: Ensembl: part 1

Wednesday

Exploring ENSEMBL functionalities: part 2
EMBOSS (the European Molecular Biology Open Software Suite):
Alignments, global, local
Searching with motifs and more
Multiple alignments
Introduction to Phylogenetics

Thursday

Introduction to the Galaxy platform
NGS data quality control
NGS genome mapping/SNP analysis
NGS RNA-seq

Friday

NGS Metagenomic data analysis
Using a Bioinformatics "Graphic User Interface"

Training Materials Availability:

Training materials for this course are not currently available.

past , bioinformatics introduction

H3ABioNet Technical Training Course (University of Pretoria, South Africa): 3 - 14 June 2013

: Training; 08 December 2013; Hits: 11243

past , sysadmin and technical

H3ABioNet Train-the-Trainer Bioinformatics Course 8th – 26th July 2013 International Center for Insect Physiology and Ecology (ICIPE), Nairobi, Kenya

: Training; 08 December 2013; Hits: 10113

Course Overview: The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. The H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent. To achieve this vision the H3ABioNet will be hosting the first specialized bioinformatics training course for bioinformaticians and researchers within the network.

The course is aimed at developing a core set of specialised skills amongst members in the network who are in a position to train others at their institutions. The course will train members who are required to efficiently manage and analyse the vast amount of genomic data generated by the various H3Africa projects.

The course will be run over 3 weeks (6 days a week) and will cover both theoretical and practical aspects of a range of topics centered on the analysis of genomic and population-based data. An emphasis will be placed on allowing participants to develop hands-on experience with analysing real data using open source software, tools and resources.

The course is open to all members within the H3A Bioinformatics Network, who have long term positions at one of the partner institutions and the capacity to train others in their institution when they return from the course.

Course objectives

The course is composed of a range of topics aimed at providing participants with the necessary hands-on practical skills to be able to manage and analyse genomic data. As well as specialized topics in population genetics, GWAS and next-generation sequence analysis, the course will include programming to ensure participants gain basic skills in data manipulation and management, and biostatistics to prepare them for statistical analysis of data.

Course outline

Programming using python – basic introduction through to advanced topics for managing and manipulating biological data. Will be run for 2 hours every morning for the duration of the course.

Introduction to Linux – basic history and introduction through to complex commands for manipulating data and Bash scripting

Data management – building simple MySQL queries and introduction to BioMart

Biostatistics – basic probability theory, introduction to R, statistical hypothesis testing, principal component analysis, building regression models and visualisation

Population genetics – content to be confirmed

Genome-wide association studies – content to be confirmed

Next-generation sequencing – introduction and QC, assembly and reference genome alignment, variant calling, RNA-seq data analysis, ChIP-seq data analysis, genome visualisation

Course prerequisites

Each course component will have prerequisites that participants will be required to complete or fulfill before the course starts. Participants will be notified of these requirements before the course commences.

How to apply

To apply to attend the course please complete the application form found here:

http://surveys.h3abionet.org/icipe

The deadline for applications is the 17th May 2013.

Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached.

For those who are unable to attend the course in person, there will be the possible option of joining the course via live streaming to Tunis (Institut Pasteur) and IBADAN (NABDA-Southwest Center, University of Ibadan).

Training Materials Availability:

Training materials for this course are not currently available.

past , education

H3ABioNet Grants Management Course - 27-28th May 2013, University of Cape Town, South Africa

: Training; 08 December 2013; Hits: 9352

Course Overview: The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. The H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers, but also to build local expertise and infrastructure. To achieve this, H3ABioNet will be hosting a short workshop on NIH grants management.

The course will be run over 2 days, and will be open to members of the H3A Bioinformatics Network, who are involved in the management of the H3ABioNet grant at each partner institution. It will be run by the NHGRI grant officials: Chris Darby and Lisa Oken.